Align Serine transporter, SerP2 or YdgB, of 459 aas and 12 TMSs (Trip et al. 2013). Transports L-alanine (Km = 20 μM), D-alanine (Km = 38 μM), L-serine, D-serine (Km = 356 μM) and glycine (Noens and Lolkema 2015). The encoding gene is adjacent to the one encoding SerP1 (TC# 2.A.3.1.21) (characterized)
to candidate WP_084935844.1 HA51_RS17310 proline-specific permease ProY
Query= TCDB::F2HQ24 (457 letters) >NCBI__GCF_002095475.1:WP_084935844.1 Length = 451 Score = 295 bits (755), Expect = 2e-84 Identities = 155/440 (35%), Positives = 247/440 (56%), Gaps = 6/440 (1%) Query: 7 EENKPSQRGLKNRHIQLIAIAGTIGTGLFLGAGKSIHLTGPSIIFVYLIIGALMYILLRA 66 +E +RGL RHI+ +A+ IGTGLF G+ +I + GPS++ Y+I GA+ YI++RA Sbjct: 2 QETNKLKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGAIAYIIMRA 61 Query: 67 IGEMLYQDPNQHSFLNFVSRYLGEKPGYFIQWSYLLVVVFVAMAELIAIGTYINFWLPDL 126 +GEM +P SF + YLG GY W+Y ++ VA+A++ A G Y+ W P++ Sbjct: 62 LGEMSVNNPQASSFSRYAQDYLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPEV 121 Query: 127 PIWMTEVFVLVLLTLLNTLNPKFFGETEFWFGMIKIVAIIGLILTAIILIFSHYHTGTDT 186 P W+ + V++++ +N ++ K FGE EFWF K+ II +IL +IF G Sbjct: 122 PHWIWVLSVVLIIGGINLMSVKVFGEVEFWFSFFKVATIIIMILAGFGIIFWGIGNGGQP 181 Query: 187 VSVTNITKGFEFFPNGLSNFFESFQMVMFAFVSMEFIGMTAAETDNPRPTLKKAINQIPI 246 + N+ FF +G+ S QMVMFA+ +E IG+TA E ++P ++ +AIN +P+ Sbjct: 182 TGIHNLWSNGGFFAHGIVGMLLSLQMVMFAYGGIEIIGITAGEAEDPAKSIPRAINSVPL 241 Query: 247 RIVLFYVGALLAIMSIYQWRDIPADKSPFVTIFQLIGIKWAAALVNFVVLTSAASALNSA 306 RI++FYVG L IMSIY W + SPFV FQ +GI AA+L+NFVV+T++ SA+NS Sbjct: 242 RILVFYVGTLFVIMSIYPWNQVGTQGSPFVLTFQHLGIAAAASLLNFVVITASLSAINSD 301 Query: 307 LFSITRNLYSLSKLNNDKILKPFTKFSKAGVPVNALLFTSLLILFTPFISMIPAISNSFV 366 +F + R L+ +++ + K FT S G P ++ + +L +++ + F+ Sbjct: 302 VFGVGRMLHGMAQQGHAP--KVFTNTSDRGAPWVTVVVMMVALLMAVYLNYLMP-EKVFL 358 Query: 367 FITSVATNLFLVVYLMTLITYLKYRKSSDFDPKG---FVLPAAHIFIPLAIAGFVLIFIS 423 I S+AT + V++M L++ + +R+ G F LP + +A V I Sbjct: 359 VIASLATFATVWVWIMILLSQIAFRRKIGAQEAGKLQFALPGGSATAWVGVAFLVFIIAL 418 Query: 424 LFCFKDTIVPAIGSVIWVLI 443 + F DT V W+L+ Sbjct: 419 IGYFPDTRVSLYAGFAWILL 438 Lambda K H 0.330 0.144 0.431 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 534 Number of extensions: 33 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 457 Length of database: 451 Length adjustment: 33 Effective length of query: 424 Effective length of database: 418 Effective search space: 177232 Effective search space used: 177232 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory